Multiple sequence alignment - TraesCS3B01G270200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G270200 chr3B 100.000 4982 0 0 2432 7413 434982440 434987421 0.000000e+00 9201.0
1 TraesCS3B01G270200 chr3B 100.000 2183 0 0 1 2183 434980009 434982191 0.000000e+00 4032.0
2 TraesCS3B01G270200 chr3D 96.183 4978 124 20 2449 7413 337305398 337310322 0.000000e+00 8080.0
3 TraesCS3B01G270200 chr3D 92.349 2222 84 46 1 2183 337303198 337305372 0.000000e+00 3083.0
4 TraesCS3B01G270200 chr3D 92.000 100 6 2 4511 4608 84113329 84113428 1.000000e-28 139.0
5 TraesCS3B01G270200 chr3A 95.866 2830 66 27 4594 7413 454514193 454516981 0.000000e+00 4530.0
6 TraesCS3B01G270200 chr3A 90.144 2222 86 33 1 2183 454510023 454512150 0.000000e+00 2767.0
7 TraesCS3B01G270200 chr3A 95.463 1124 22 6 3414 4514 454513076 454514193 0.000000e+00 1766.0
8 TraesCS3B01G270200 chr3A 96.820 912 22 4 2449 3356 454512176 454513084 0.000000e+00 1517.0
9 TraesCS3B01G270200 chr6D 86.441 177 21 3 3345 3520 41929215 41929041 2.730000e-44 191.0
10 TraesCS3B01G270200 chr6D 85.417 96 12 2 7190 7284 429020980 429020886 1.700000e-16 99.0
11 TraesCS3B01G270200 chr6A 85.795 176 22 3 3343 3518 52399585 52399413 4.570000e-42 183.0
12 TraesCS3B01G270200 chr7D 84.615 182 26 2 3338 3518 414518667 414518847 5.910000e-41 180.0
13 TraesCS3B01G270200 chr7D 93.684 95 5 1 4506 4600 22964253 22964346 2.790000e-29 141.0
14 TraesCS3B01G270200 chr7D 89.474 95 10 0 7190 7284 509615411 509615317 3.630000e-23 121.0
15 TraesCS3B01G270200 chr2B 84.358 179 26 2 3341 3518 414793534 414793357 2.750000e-39 174.0
16 TraesCS3B01G270200 chr2B 83.799 179 27 2 3341 3518 415057859 415057682 1.280000e-37 169.0
17 TraesCS3B01G270200 chr2B 92.784 97 7 0 4501 4597 575147082 575146986 2.790000e-29 141.0
18 TraesCS3B01G270200 chr2B 100.000 28 0 0 7334 7361 635024389 635024416 1.300000e-02 52.8
19 TraesCS3B01G270200 chr1B 84.358 179 26 2 3341 3518 268403574 268403397 2.750000e-39 174.0
20 TraesCS3B01G270200 chr6B 83.516 182 28 2 3338 3518 84057399 84057579 1.280000e-37 169.0
21 TraesCS3B01G270200 chr6B 93.684 95 4 2 4511 4605 8403550 8403642 2.790000e-29 141.0
22 TraesCS3B01G270200 chr6B 87.368 95 8 4 7190 7282 568477410 568477502 1.020000e-18 106.0
23 TraesCS3B01G270200 chr6B 86.170 94 11 1 7190 7281 549621290 549621383 4.730000e-17 100.0
24 TraesCS3B01G270200 chr1D 83.516 182 28 2 3338 3518 249720088 249720268 1.280000e-37 169.0
25 TraesCS3B01G270200 chr1D 95.556 90 2 2 4511 4599 335585040 335585128 7.750000e-30 143.0
26 TraesCS3B01G270200 chr1A 93.939 99 6 0 4504 4602 505133989 505133891 4.630000e-32 150.0
27 TraesCS3B01G270200 chr4A 95.556 90 4 0 4510 4599 556767954 556768043 2.160000e-30 145.0
28 TraesCS3B01G270200 chr4A 85.263 95 14 0 7187 7281 601172077 601172171 1.700000e-16 99.0
29 TraesCS3B01G270200 chr7A 94.565 92 5 0 4504 4595 467851913 467851822 7.750000e-30 143.0
30 TraesCS3B01G270200 chr7A 91.304 92 8 0 7190 7281 547102798 547102889 7.810000e-25 126.0
31 TraesCS3B01G270200 chr5D 90.000 110 7 4 4511 4620 240428042 240428147 1.000000e-28 139.0
32 TraesCS3B01G270200 chrUn 89.247 93 10 0 7192 7284 60938277 60938369 4.700000e-22 117.0
33 TraesCS3B01G270200 chr2D 100.000 28 0 0 7334 7361 534311126 534311153 1.300000e-02 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G270200 chr3B 434980009 434987421 7412 False 6616.5 9201 100.00000 1 7413 2 chr3B.!!$F1 7412
1 TraesCS3B01G270200 chr3D 337303198 337310322 7124 False 5581.5 8080 94.26600 1 7413 2 chr3D.!!$F2 7412
2 TraesCS3B01G270200 chr3A 454510023 454516981 6958 False 2645.0 4530 94.57325 1 7413 4 chr3A.!!$F1 7412

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
271 280 0.038526 CTGCTGTACTCCGTTCCGTT 60.039 55.000 0.00 0.0 0.00 4.44 F
272 281 0.038892 TGCTGTACTCCGTTCCGTTC 60.039 55.000 0.00 0.0 0.00 3.95 F
733 795 0.315251 GCTCCTTGTGTTTGCCCTTC 59.685 55.000 0.00 0.0 0.00 3.46 F
1991 2068 0.108207 CCTCATAGCTGGAGGCCAAG 59.892 60.000 19.56 0.0 44.95 3.61 F
1993 2070 0.326522 TCATAGCTGGAGGCCAAGGA 60.327 55.000 5.01 0.0 43.05 3.36 F
1994 2071 0.548031 CATAGCTGGAGGCCAAGGAA 59.452 55.000 5.01 0.0 43.05 3.36 F
2698 2777 0.843309 TGGAAAGGTTCTCCACTGCA 59.157 50.000 0.00 0.0 38.07 4.41 F
4527 4631 0.178970 GCTACTCCCCTCGTCCCATA 60.179 60.000 0.00 0.0 0.00 2.74 F
6073 6180 1.227823 CAGTCAACGAAGGGTGGCA 60.228 57.895 0.00 0.0 0.00 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 1703 1.149101 AGGAGTTGGAAAGGCCTCAA 58.851 50.000 5.23 2.83 37.63 3.02 R
1677 1754 1.637553 AGGTTGCATCTGAATCACCCT 59.362 47.619 0.00 0.00 0.00 4.34 R
2444 2522 0.251209 GAAGTTGAACCCAGGTCCCC 60.251 60.000 0.00 0.00 0.00 4.81 R
3077 3156 0.179018 ACTGGTGGTGCTCTTTGGTC 60.179 55.000 0.00 0.00 0.00 4.02 R
3403 3484 1.439679 AGTTGCGCTTAAGTGTAGGC 58.560 50.000 17.00 9.59 0.00 3.93 R
3405 3486 5.541766 CGTATAGTTGCGCTTAAGTGTAG 57.458 43.478 17.00 2.05 0.00 2.74 R
4533 4637 3.793559 ACACTAGTGTCAAAAACGCTCT 58.206 40.909 22.95 0.00 45.69 4.09 R
6193 6300 1.647545 CCATGAAACGCTGCATCGGT 61.648 55.000 15.16 4.39 0.00 4.69 R
6965 7073 2.316108 CAACAACCCCCAAAACTAGCT 58.684 47.619 0.00 0.00 0.00 3.32 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 9.406113 AGAAAGGAAAAGAAGATGGATGATTAG 57.594 33.333 0.00 0.00 0.00 1.73
121 122 6.443206 AGACCTTATCCTGCTGCTATGAATAT 59.557 38.462 0.00 0.00 0.00 1.28
160 161 2.649312 AGAAATCCAGATCCACCAACCA 59.351 45.455 0.00 0.00 0.00 3.67
170 171 6.263168 CCAGATCCACCAACCAATAAGATAAC 59.737 42.308 0.00 0.00 0.00 1.89
171 172 6.263168 CAGATCCACCAACCAATAAGATAACC 59.737 42.308 0.00 0.00 0.00 2.85
175 176 2.286772 CCAACCAATAAGATAACCGCGC 60.287 50.000 0.00 0.00 0.00 6.86
177 178 2.914059 ACCAATAAGATAACCGCGCTT 58.086 42.857 5.56 0.00 0.00 4.68
196 197 2.806608 TTCTTATCGTATCACGGCCC 57.193 50.000 0.00 0.00 42.81 5.80
228 229 1.492319 CGAAACTTCCCACGCGAACA 61.492 55.000 15.93 0.00 0.00 3.18
239 240 3.782042 GCGAACAGAACCGCCTAG 58.218 61.111 0.00 0.00 45.06 3.02
240 241 1.080025 GCGAACAGAACCGCCTAGT 60.080 57.895 0.00 0.00 45.06 2.57
241 242 1.352156 GCGAACAGAACCGCCTAGTG 61.352 60.000 0.00 0.00 45.06 2.74
267 276 5.407387 TCATTTTTACTGCTGTACTCCGTTC 59.593 40.000 2.52 0.00 0.00 3.95
268 277 3.308438 TTTACTGCTGTACTCCGTTCC 57.692 47.619 2.52 0.00 0.00 3.62
269 278 0.806868 TACTGCTGTACTCCGTTCCG 59.193 55.000 0.00 0.00 0.00 4.30
270 279 1.177256 ACTGCTGTACTCCGTTCCGT 61.177 55.000 0.00 0.00 0.00 4.69
271 280 0.038526 CTGCTGTACTCCGTTCCGTT 60.039 55.000 0.00 0.00 0.00 4.44
272 281 0.038892 TGCTGTACTCCGTTCCGTTC 60.039 55.000 0.00 0.00 0.00 3.95
416 441 4.862018 GCAAGCTGAACAAAAGTGTGTTAA 59.138 37.500 0.00 0.00 41.78 2.01
419 444 7.382218 GCAAGCTGAACAAAAGTGTGTTAATAT 59.618 33.333 0.00 0.00 41.78 1.28
606 634 3.243068 GCGGCTGTCAAAAGAAAGAAAGA 60.243 43.478 0.00 0.00 0.00 2.52
607 635 4.733523 GCGGCTGTCAAAAGAAAGAAAGAA 60.734 41.667 0.00 0.00 0.00 2.52
608 636 5.339990 CGGCTGTCAAAAGAAAGAAAGAAA 58.660 37.500 0.00 0.00 0.00 2.52
609 637 5.456822 CGGCTGTCAAAAGAAAGAAAGAAAG 59.543 40.000 0.00 0.00 0.00 2.62
662 690 3.775654 CCTGCCCGAGGACCAGTC 61.776 72.222 0.00 0.00 46.33 3.51
663 691 2.997315 CTGCCCGAGGACCAGTCA 60.997 66.667 0.00 0.00 0.00 3.41
664 692 2.997315 TGCCCGAGGACCAGTCAG 60.997 66.667 0.00 0.00 0.00 3.51
665 693 2.997897 GCCCGAGGACCAGTCAGT 60.998 66.667 0.00 0.00 0.00 3.41
666 694 3.007973 GCCCGAGGACCAGTCAGTC 62.008 68.421 0.00 0.00 35.95 3.51
667 695 2.701780 CCCGAGGACCAGTCAGTCG 61.702 68.421 12.44 12.44 37.66 4.18
733 795 0.315251 GCTCCTTGTGTTTGCCCTTC 59.685 55.000 0.00 0.00 0.00 3.46
734 796 1.691196 CTCCTTGTGTTTGCCCTTCA 58.309 50.000 0.00 0.00 0.00 3.02
858 921 3.119096 GAGCGTTCCGGTTCAGGC 61.119 66.667 0.00 4.45 37.83 4.85
898 965 1.950973 TTTCATCGTCGATCCGCCCA 61.951 55.000 4.34 0.00 0.00 5.36
967 1038 3.053291 GGCGGTGACAAATGCGGA 61.053 61.111 0.00 0.00 0.00 5.54
980 1051 2.895372 GCGGATTGATTCGCCGGT 60.895 61.111 1.90 0.00 45.42 5.28
1017 1088 4.349503 ATGCAGCCGGACCAGCAA 62.350 61.111 5.05 0.00 40.76 3.91
1020 1091 2.594303 CAGCCGGACCAGCAACAA 60.594 61.111 5.05 0.00 0.00 2.83
1021 1092 2.594592 AGCCGGACCAGCAACAAC 60.595 61.111 5.05 0.00 0.00 3.32
1022 1093 2.904866 GCCGGACCAGCAACAACA 60.905 61.111 5.05 0.00 0.00 3.33
1135 1211 2.202756 GGCGCTTCGAGATCGGTT 60.203 61.111 7.64 0.00 40.29 4.44
1136 1212 2.231618 GGCGCTTCGAGATCGGTTC 61.232 63.158 7.64 0.00 40.29 3.62
1171 1247 1.335132 TGGATGAACCTACCTCGCCC 61.335 60.000 0.00 0.00 39.86 6.13
1220 1297 3.924013 ATGACGAGGGGGCACTGGA 62.924 63.158 0.00 0.00 0.00 3.86
1279 1356 5.517904 GTCAGAATTATCTCTTGCCATTGC 58.482 41.667 0.00 0.00 32.03 3.56
1326 1403 2.353803 CGTCGACAATTCCTTCCTTCCT 60.354 50.000 17.16 0.00 0.00 3.36
1328 1405 3.685272 GTCGACAATTCCTTCCTTCCTTC 59.315 47.826 11.55 0.00 0.00 3.46
1329 1406 3.010420 CGACAATTCCTTCCTTCCTTCC 58.990 50.000 0.00 0.00 0.00 3.46
1330 1407 3.010420 GACAATTCCTTCCTTCCTTCCG 58.990 50.000 0.00 0.00 0.00 4.30
1331 1408 2.375509 ACAATTCCTTCCTTCCTTCCGT 59.624 45.455 0.00 0.00 0.00 4.69
1332 1409 3.181433 ACAATTCCTTCCTTCCTTCCGTT 60.181 43.478 0.00 0.00 0.00 4.44
1333 1410 3.808834 ATTCCTTCCTTCCTTCCGTTT 57.191 42.857 0.00 0.00 0.00 3.60
1402 1479 8.519492 TTTCTTCCATTTCTTATTGCGAAAAG 57.481 30.769 0.00 0.00 34.42 2.27
1450 1527 9.281371 TCTGGATCACAATTCATCTCAATTATC 57.719 33.333 0.00 0.00 0.00 1.75
1512 1589 2.675348 CCTGAAATCTTCTTCTGCGGTC 59.325 50.000 0.00 0.00 0.00 4.79
1538 1615 1.285950 GGCACCGTCTTTTCTTGCC 59.714 57.895 0.00 0.00 45.64 4.52
1626 1703 5.003804 ACTCATTGCTTCGTAAAGGATTGT 58.996 37.500 0.00 0.00 36.31 2.71
1637 1714 4.379499 CGTAAAGGATTGTTGAGGCCTTTC 60.379 45.833 6.77 0.71 45.01 2.62
1778 1855 2.174639 ACTCAACCCAATTCTGTGGTCA 59.825 45.455 0.00 0.00 36.90 4.02
1990 2067 2.224821 CCTCATAGCTGGAGGCCAA 58.775 57.895 19.56 0.00 44.95 4.52
1991 2068 0.108207 CCTCATAGCTGGAGGCCAAG 59.892 60.000 19.56 0.00 44.95 3.61
1992 2069 0.108207 CTCATAGCTGGAGGCCAAGG 59.892 60.000 5.01 0.00 43.05 3.61
1993 2070 0.326522 TCATAGCTGGAGGCCAAGGA 60.327 55.000 5.01 0.00 43.05 3.36
1994 2071 0.548031 CATAGCTGGAGGCCAAGGAA 59.452 55.000 5.01 0.00 43.05 3.36
1995 2072 1.144503 CATAGCTGGAGGCCAAGGAAT 59.855 52.381 5.01 0.00 43.05 3.01
2000 2077 1.846439 CTGGAGGCCAAGGAATAGGAA 59.154 52.381 5.01 0.00 30.80 3.36
2013 2090 5.200483 AGGAATAGGAATTTTGCATCGGAA 58.800 37.500 0.00 0.00 0.00 4.30
2094 2172 5.356882 TTTTGTGCTGTATACAACTCTGC 57.643 39.130 7.06 7.03 37.73 4.26
2095 2173 3.676291 TGTGCTGTATACAACTCTGCA 57.324 42.857 11.49 11.49 0.00 4.41
2487 2565 9.567848 TTCTTTTTGTCATCTAAGTTGTTTCAC 57.432 29.630 0.00 0.00 0.00 3.18
2564 2643 3.243535 GCTGAACCTTTTCTGGTCCTTTG 60.244 47.826 0.00 0.00 39.83 2.77
2611 2690 2.751259 GCCATCTGACATTGAGCTCAAA 59.249 45.455 31.55 15.49 39.55 2.69
2640 2719 9.547753 TTGAGGCAGATATTACTCAGTAAATTC 57.452 33.333 0.16 1.96 40.63 2.17
2698 2777 0.843309 TGGAAAGGTTCTCCACTGCA 59.157 50.000 0.00 0.00 38.07 4.41
2713 2792 4.526650 TCCACTGCACAGTATTAACTCTGA 59.473 41.667 2.38 0.00 40.20 3.27
3077 3156 1.522668 TCAAGGCCAACGATGACTTG 58.477 50.000 17.66 17.66 40.06 3.16
3188 3267 5.361285 AGATCGGAGTTAGCATACAGTTCTT 59.639 40.000 0.00 0.00 0.00 2.52
3190 3269 5.168569 TCGGAGTTAGCATACAGTTCTTTG 58.831 41.667 0.00 0.00 0.00 2.77
3328 3409 7.811236 AGAAATGCACTCACACATAAAATTCAG 59.189 33.333 0.00 0.00 0.00 3.02
3358 3439 4.038763 GCCAAAGTTAAAAAGGCACTAGGT 59.961 41.667 0.00 0.00 44.59 3.08
3377 3458 2.219903 GGTGTTAATTGTGCGTTTTGCC 59.780 45.455 0.00 0.00 45.60 4.52
3541 3629 4.316025 AGTGCTAACCCAATAACCATGT 57.684 40.909 0.00 0.00 0.00 3.21
3992 4080 6.740411 TGGACGGTATGTAAATTTTGGTAC 57.260 37.500 0.00 0.00 0.00 3.34
4209 4297 2.472695 TCTTGTGCGCTACTTTCCAT 57.527 45.000 9.73 0.00 0.00 3.41
4271 4359 9.734620 GCTGTTTAATATCACATTATTCTTGCA 57.265 29.630 0.00 0.00 0.00 4.08
4525 4629 2.043248 GCTACTCCCCTCGTCCCA 60.043 66.667 0.00 0.00 0.00 4.37
4526 4630 1.457831 GCTACTCCCCTCGTCCCAT 60.458 63.158 0.00 0.00 0.00 4.00
4527 4631 0.178970 GCTACTCCCCTCGTCCCATA 60.179 60.000 0.00 0.00 0.00 2.74
4528 4632 1.756690 GCTACTCCCCTCGTCCCATAA 60.757 57.143 0.00 0.00 0.00 1.90
4529 4633 2.890814 CTACTCCCCTCGTCCCATAAT 58.109 52.381 0.00 0.00 0.00 1.28
4530 4634 3.816842 GCTACTCCCCTCGTCCCATAATA 60.817 52.174 0.00 0.00 0.00 0.98
4531 4635 3.562108 ACTCCCCTCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
4532 4636 4.687262 ACTCCCCTCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
4533 4637 5.019657 ACTCCCCTCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
4534 4638 5.024118 ACTCCCCTCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
4535 4639 5.222484 ACTCCCCTCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
4536 4640 5.269991 TCCCCTCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
4537 4641 4.141914 CCCCTCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
4538 4642 4.440250 CCCTCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
4539 4643 4.158025 CCTCGTCCCATAATATAAGAGCGT 59.842 45.833 0.00 0.00 0.00 5.07
4540 4644 5.336531 CCTCGTCCCATAATATAAGAGCGTT 60.337 44.000 0.00 0.00 0.00 4.84
4541 4645 6.092955 TCGTCCCATAATATAAGAGCGTTT 57.907 37.500 0.00 0.00 0.00 3.60
4542 4646 6.518493 TCGTCCCATAATATAAGAGCGTTTT 58.482 36.000 0.00 0.00 0.00 2.43
4543 4647 6.987992 TCGTCCCATAATATAAGAGCGTTTTT 59.012 34.615 0.00 0.00 0.00 1.94
4544 4648 7.042321 TCGTCCCATAATATAAGAGCGTTTTTG 60.042 37.037 0.00 0.00 0.00 2.44
4545 4649 7.042321 CGTCCCATAATATAAGAGCGTTTTTGA 60.042 37.037 0.00 0.00 0.00 2.69
4546 4650 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
4547 4651 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
4548 4652 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
4549 4653 8.612619 CCATAATATAAGAGCGTTTTTGACACT 58.387 33.333 0.00 0.00 0.00 3.55
4586 4690 8.783093 CAAAAACGCTCTTATATTATGGGATGA 58.217 33.333 0.00 0.00 0.00 2.92
5051 5157 1.913419 GACCCCAAGGATAGACCAACA 59.087 52.381 0.00 0.00 42.04 3.33
5083 5189 8.594550 AGAGGCAAGTGTTTCTAGATAAAACTA 58.405 33.333 9.52 0.00 37.48 2.24
5152 5258 3.002038 TGTGCACATCATAATCAGGCA 57.998 42.857 17.42 0.00 0.00 4.75
5469 5576 2.699954 AGTGCTGTAGACAATTTCCGG 58.300 47.619 0.00 0.00 0.00 5.14
5669 5776 8.341892 TGTGTGCATGGTTAAAATATAGTTCA 57.658 30.769 0.00 0.00 0.00 3.18
5702 5809 5.297547 TCATGGTACTATGGAATCGCTTTC 58.702 41.667 18.03 0.00 0.00 2.62
5760 5867 5.176223 CAGTTCAAGTTTGATGATTTGGCAC 59.824 40.000 0.00 0.00 37.00 5.01
5874 5981 4.699257 CCAAAAGATCAGAAGTCTTCCCAG 59.301 45.833 9.04 0.41 34.97 4.45
5958 6065 5.314718 TCTTCAGATGGCACCAATATGAT 57.685 39.130 0.00 0.00 0.00 2.45
5966 6073 9.788889 CAGATGGCACCAATATGATATGTATAT 57.211 33.333 0.00 0.00 0.00 0.86
6073 6180 1.227823 CAGTCAACGAAGGGTGGCA 60.228 57.895 0.00 0.00 0.00 4.92
6193 6300 0.036164 AAGACCGCATGCAGTACCAA 59.964 50.000 19.57 0.00 0.00 3.67
6413 6520 8.822805 AGTATGGAGTTTCAAGGATGTACTAAA 58.177 33.333 0.00 0.00 0.00 1.85
6429 6536 8.613060 ATGTACTAAATGATCTAGTGCAATGG 57.387 34.615 12.97 0.00 42.68 3.16
6431 6538 5.688807 ACTAAATGATCTAGTGCAATGGCT 58.311 37.500 0.00 0.00 41.91 4.75
6460 6567 2.795231 ATGCTTGGCTTAGCTGAAGA 57.205 45.000 16.68 6.14 41.76 2.87
6502 6609 6.405508 CGAAGTACTTCCTGAGTTGCCTTATA 60.406 42.308 26.12 0.00 39.86 0.98
6536 6643 4.403752 TCAGACAGTGGATCGATGATCTTT 59.596 41.667 0.54 0.00 38.91 2.52
6561 6668 2.478709 CGAGGAGGAAGTTGATGTCTCG 60.479 54.545 0.00 0.00 37.21 4.04
6570 6677 4.322080 AGTTGATGTCTCGTGAAGAACA 57.678 40.909 0.00 0.00 35.21 3.18
6604 6711 9.851686 ATAAGATTATGCAAAGACAACATCCTA 57.148 29.630 0.00 0.00 0.00 2.94
6646 6753 6.127897 CCAAGGAAAGAATGACATCTGGTAAC 60.128 42.308 0.00 0.00 0.00 2.50
6723 6830 7.090953 TGTACTTTGAAAGAACGGAAACATT 57.909 32.000 12.53 0.00 0.00 2.71
6791 6898 6.870971 TTTTTCTTTGTATTACTGTCGGCT 57.129 33.333 0.00 0.00 0.00 5.52
6957 7065 6.599638 ACCAAACTTCAGTAAGATAGAATGGC 59.400 38.462 0.00 0.00 36.50 4.40
6965 7073 7.337938 TCAGTAAGATAGAATGGCAATGAACA 58.662 34.615 0.00 0.00 0.00 3.18
7076 7184 9.533831 AGGTACTGATCATTTCCAAATTAACTT 57.466 29.630 10.67 0.00 37.18 2.66
7097 7205 8.494016 AACTTAATGTCTAGCCTTGTCATAAC 57.506 34.615 0.00 0.00 0.00 1.89
7098 7206 7.852263 ACTTAATGTCTAGCCTTGTCATAACT 58.148 34.615 0.00 0.00 0.00 2.24
7099 7207 8.322091 ACTTAATGTCTAGCCTTGTCATAACTT 58.678 33.333 0.00 0.00 0.00 2.66
7100 7208 9.817809 CTTAATGTCTAGCCTTGTCATAACTTA 57.182 33.333 0.00 0.00 0.00 2.24
7103 7211 7.900782 TGTCTAGCCTTGTCATAACTTAAAC 57.099 36.000 0.00 0.00 0.00 2.01
7104 7212 7.676947 TGTCTAGCCTTGTCATAACTTAAACT 58.323 34.615 0.00 0.00 0.00 2.66
7105 7213 8.154856 TGTCTAGCCTTGTCATAACTTAAACTT 58.845 33.333 0.00 0.00 0.00 2.66
7106 7214 9.000486 GTCTAGCCTTGTCATAACTTAAACTTT 58.000 33.333 0.00 0.00 0.00 2.66
7107 7215 9.569122 TCTAGCCTTGTCATAACTTAAACTTTT 57.431 29.630 0.00 0.00 0.00 2.27
7165 7273 6.238211 GCAAGACCACACTACATTCATCATAC 60.238 42.308 0.00 0.00 0.00 2.39
7255 7369 9.825972 CATACGAACTAAAATGAGTGAACAAAT 57.174 29.630 0.00 0.00 0.00 2.32
7271 7385 9.120538 AGTGAACAAATACACTAAAATGTGTCT 57.879 29.630 3.46 0.00 46.90 3.41
7289 7403 9.775854 AATGTGTCTATATCCATCTGAGAAAAG 57.224 33.333 0.00 0.00 0.00 2.27
7344 7458 6.128634 GGAGTAGAACTTGTATTTGTGAACGG 60.129 42.308 0.00 0.00 0.00 4.44
7352 7466 3.833650 TGTATTTGTGAACGGAGGGAGTA 59.166 43.478 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 3.318539 CTCGCATGTGCTGTGGTGC 62.319 63.158 0.00 0.00 39.32 5.01
56 57 1.265905 CGCCAAATAACCTAATCGGGC 59.734 52.381 0.00 0.00 36.97 6.13
121 122 6.600822 GGATTTCTTCCATCTCATCTCAACAA 59.399 38.462 0.00 0.00 44.74 2.83
160 161 6.128902 CGATAAGAAAGCGCGGTTATCTTATT 60.129 38.462 35.44 27.89 41.16 1.40
170 171 2.153247 GTGATACGATAAGAAAGCGCGG 59.847 50.000 8.83 0.00 0.00 6.46
171 172 2.160272 CGTGATACGATAAGAAAGCGCG 60.160 50.000 0.00 0.00 46.05 6.86
175 176 3.057734 GGGCCGTGATACGATAAGAAAG 58.942 50.000 2.52 0.00 46.05 2.62
177 178 1.342174 GGGGCCGTGATACGATAAGAA 59.658 52.381 2.52 0.00 46.05 2.52
239 240 5.390991 GGAGTACAGCAGTAAAAATGAGCAC 60.391 44.000 0.00 0.00 30.67 4.40
240 241 4.695455 GGAGTACAGCAGTAAAAATGAGCA 59.305 41.667 0.00 0.00 30.67 4.26
241 242 4.201724 CGGAGTACAGCAGTAAAAATGAGC 60.202 45.833 0.00 0.00 30.67 4.26
267 276 2.095372 GCACCTTTTTCTATCCGAACGG 59.905 50.000 6.94 6.94 0.00 4.44
268 277 2.222729 CGCACCTTTTTCTATCCGAACG 60.223 50.000 0.00 0.00 0.00 3.95
269 278 2.095372 CCGCACCTTTTTCTATCCGAAC 59.905 50.000 0.00 0.00 0.00 3.95
270 279 2.027929 TCCGCACCTTTTTCTATCCGAA 60.028 45.455 0.00 0.00 0.00 4.30
271 280 1.551430 TCCGCACCTTTTTCTATCCGA 59.449 47.619 0.00 0.00 0.00 4.55
272 281 2.018542 TCCGCACCTTTTTCTATCCG 57.981 50.000 0.00 0.00 0.00 4.18
471 498 0.314935 CAGGCATGCGTTTTTCTGGT 59.685 50.000 10.81 0.00 0.00 4.00
606 634 3.531934 AAAGAAGTGCTTGCTTGCTTT 57.468 38.095 3.47 0.00 36.80 3.51
607 635 3.531934 AAAAGAAGTGCTTGCTTGCTT 57.468 38.095 3.47 0.00 36.80 3.91
608 636 3.531934 AAAAAGAAGTGCTTGCTTGCT 57.468 38.095 3.47 0.00 36.80 3.91
609 637 4.317348 CGTTAAAAAGAAGTGCTTGCTTGC 60.317 41.667 0.00 0.00 36.80 4.01
645 673 3.775654 GACTGGTCCTCGGGCAGG 61.776 72.222 0.00 0.00 45.15 4.85
647 675 2.997315 CTGACTGGTCCTCGGGCA 60.997 66.667 0.00 0.00 37.45 5.36
649 677 2.701780 CGACTGACTGGTCCTCGGG 61.702 68.421 8.92 0.00 33.07 5.14
650 678 2.878429 CGACTGACTGGTCCTCGG 59.122 66.667 8.92 0.00 33.07 4.63
651 679 2.179517 GCGACTGACTGGTCCTCG 59.820 66.667 11.24 11.24 34.08 4.63
652 680 2.574399 GGCGACTGACTGGTCCTC 59.426 66.667 0.00 0.00 33.07 3.71
653 681 3.374402 CGGCGACTGACTGGTCCT 61.374 66.667 0.00 0.00 33.07 3.85
654 682 2.927580 TTCGGCGACTGACTGGTCC 61.928 63.158 10.16 0.00 33.07 4.46
655 683 1.733399 GTTCGGCGACTGACTGGTC 60.733 63.158 10.16 0.00 0.00 4.02
656 684 2.338984 GTTCGGCGACTGACTGGT 59.661 61.111 10.16 0.00 0.00 4.00
657 685 2.805353 CGTTCGGCGACTGACTGG 60.805 66.667 10.16 0.00 44.77 4.00
658 686 2.254350 TCGTTCGGCGACTGACTG 59.746 61.111 10.16 2.51 45.68 3.51
666 694 3.252484 GATCGGGTTCGTTCGGCG 61.252 66.667 0.00 0.00 43.01 6.46
967 1038 0.322098 TTGTCCACCGGCGAATCAAT 60.322 50.000 9.30 0.00 0.00 2.57
980 1051 4.680237 CTCACCGCCGCTTGTCCA 62.680 66.667 0.00 0.00 0.00 4.02
1017 1088 1.825191 CTGCTGGTGCTGGTGTTGT 60.825 57.895 0.00 0.00 40.48 3.32
1018 1089 3.036577 CTGCTGGTGCTGGTGTTG 58.963 61.111 0.00 0.00 40.48 3.33
1019 1090 2.908940 GCTGCTGGTGCTGGTGTT 60.909 61.111 0.00 0.00 40.48 3.32
1206 1283 3.775654 GAGTCCAGTGCCCCCTCG 61.776 72.222 0.00 0.00 0.00 4.63
1279 1356 4.405358 AGGAGAAGAGAAGTTGCAGGATAG 59.595 45.833 0.00 0.00 0.00 2.08
1326 1403 4.515361 TCAACAACCTCAACTAAACGGAA 58.485 39.130 0.00 0.00 0.00 4.30
1328 1405 5.432885 AATCAACAACCTCAACTAAACGG 57.567 39.130 0.00 0.00 0.00 4.44
1329 1406 6.491394 TGAAATCAACAACCTCAACTAAACG 58.509 36.000 0.00 0.00 0.00 3.60
1330 1407 6.417930 GCTGAAATCAACAACCTCAACTAAAC 59.582 38.462 0.00 0.00 0.00 2.01
1331 1408 6.321181 AGCTGAAATCAACAACCTCAACTAAA 59.679 34.615 0.00 0.00 0.00 1.85
1332 1409 5.827797 AGCTGAAATCAACAACCTCAACTAA 59.172 36.000 0.00 0.00 0.00 2.24
1333 1410 5.376625 AGCTGAAATCAACAACCTCAACTA 58.623 37.500 0.00 0.00 0.00 2.24
1402 1479 1.636003 ACAGGAGTGAAAAGGATCCCC 59.364 52.381 8.55 0.00 31.86 4.81
1450 1527 3.278574 TCCAACAGAGAACCTTGTGTTG 58.721 45.455 8.53 8.53 46.12 3.33
1626 1703 1.149101 AGGAGTTGGAAAGGCCTCAA 58.851 50.000 5.23 2.83 37.63 3.02
1637 1714 3.750371 TGGTGTTGATTACAGGAGTTGG 58.250 45.455 0.00 0.00 37.45 3.77
1677 1754 1.637553 AGGTTGCATCTGAATCACCCT 59.362 47.619 0.00 0.00 0.00 4.34
1678 1755 2.134789 AGGTTGCATCTGAATCACCC 57.865 50.000 0.00 0.00 0.00 4.61
1778 1855 4.394729 TGCAAGAAAAAGGACGGTAAGAT 58.605 39.130 0.00 0.00 0.00 2.40
1904 1981 5.589367 AGGATGTGTTCTTGGGCATATAT 57.411 39.130 0.00 0.00 0.00 0.86
1905 1982 5.387113 AAGGATGTGTTCTTGGGCATATA 57.613 39.130 0.00 0.00 0.00 0.86
1906 1983 3.959495 AGGATGTGTTCTTGGGCATAT 57.041 42.857 0.00 0.00 0.00 1.78
1990 2067 4.792068 TCCGATGCAAAATTCCTATTCCT 58.208 39.130 0.00 0.00 0.00 3.36
1991 2068 5.514274 TTCCGATGCAAAATTCCTATTCC 57.486 39.130 0.00 0.00 0.00 3.01
1992 2069 5.979517 CCTTTCCGATGCAAAATTCCTATTC 59.020 40.000 0.00 0.00 0.00 1.75
1993 2070 5.163416 CCCTTTCCGATGCAAAATTCCTATT 60.163 40.000 0.00 0.00 0.00 1.73
1994 2071 4.342092 CCCTTTCCGATGCAAAATTCCTAT 59.658 41.667 0.00 0.00 0.00 2.57
1995 2072 3.699038 CCCTTTCCGATGCAAAATTCCTA 59.301 43.478 0.00 0.00 0.00 2.94
2000 2077 2.807676 ACTCCCTTTCCGATGCAAAAT 58.192 42.857 0.00 0.00 0.00 1.82
2013 2090 1.823610 GACGGTAGCTACAACTCCCTT 59.176 52.381 24.75 0.25 0.00 3.95
2094 2172 4.696877 TGTAATCTGCATCCAACTGACTTG 59.303 41.667 0.00 0.00 0.00 3.16
2095 2173 4.910195 TGTAATCTGCATCCAACTGACTT 58.090 39.130 0.00 0.00 0.00 3.01
2443 2521 1.726192 AAGTTGAACCCAGGTCCCCC 61.726 60.000 0.00 0.00 0.00 5.40
2444 2522 0.251209 GAAGTTGAACCCAGGTCCCC 60.251 60.000 0.00 0.00 0.00 4.81
2445 2523 0.771755 AGAAGTTGAACCCAGGTCCC 59.228 55.000 0.00 0.00 0.00 4.46
2446 2524 2.658807 AAGAAGTTGAACCCAGGTCC 57.341 50.000 0.00 0.00 0.00 4.46
2447 2525 4.159693 ACAAAAAGAAGTTGAACCCAGGTC 59.840 41.667 0.00 0.00 0.00 3.85
2564 2643 3.774066 CCTGCCAGCAAATAAACTTAGC 58.226 45.455 0.00 0.00 0.00 3.09
2611 2690 4.653341 ACTGAGTAATATCTGCCTCAAGCT 59.347 41.667 0.00 0.00 44.23 3.74
2640 2719 3.074412 ACACATACAGAAAAGAAGGCCG 58.926 45.455 0.00 0.00 0.00 6.13
3077 3156 0.179018 ACTGGTGGTGCTCTTTGGTC 60.179 55.000 0.00 0.00 0.00 4.02
3169 3248 6.204882 ACAACAAAGAACTGTATGCTAACTCC 59.795 38.462 0.00 0.00 0.00 3.85
3188 3267 7.386573 TCAAGAAAGATTATAGCACGACAACAA 59.613 33.333 0.00 0.00 0.00 2.83
3190 3269 7.290857 TCAAGAAAGATTATAGCACGACAAC 57.709 36.000 0.00 0.00 0.00 3.32
3231 3310 7.501559 GCGAACTACAGATAGGGTATGGATATA 59.498 40.741 0.00 0.00 32.08 0.86
3232 3311 6.321690 GCGAACTACAGATAGGGTATGGATAT 59.678 42.308 0.00 0.00 32.08 1.63
3328 3409 5.220381 GCCTTTTTAACTTTGGCACTAGAC 58.780 41.667 0.00 0.00 42.79 2.59
3358 3439 2.860735 GTGGCAAAACGCACAATTAACA 59.139 40.909 0.00 0.00 45.17 2.41
3403 3484 1.439679 AGTTGCGCTTAAGTGTAGGC 58.560 50.000 17.00 9.59 0.00 3.93
3405 3486 5.541766 CGTATAGTTGCGCTTAAGTGTAG 57.458 43.478 17.00 2.05 0.00 2.74
3541 3629 7.201785 GGACAATTTTCTCTAAAATATGGCGGA 60.202 37.037 0.00 0.00 43.04 5.54
4256 4344 8.785329 TTACTATGTGTGCAAGAATAATGTGA 57.215 30.769 0.00 0.00 0.00 3.58
4517 4621 5.312120 ACGCTCTTATATTATGGGACGAG 57.688 43.478 0.00 0.00 0.00 4.18
4518 4622 5.717078 AACGCTCTTATATTATGGGACGA 57.283 39.130 0.00 0.00 0.00 4.20
4526 4630 9.865321 ACTAGTGTCAAAAACGCTCTTATATTA 57.135 29.630 0.00 0.00 45.69 0.98
4527 4631 8.656849 CACTAGTGTCAAAAACGCTCTTATATT 58.343 33.333 15.06 0.00 45.69 1.28
4528 4632 7.817962 ACACTAGTGTCAAAAACGCTCTTATAT 59.182 33.333 22.95 0.00 45.69 0.86
4529 4633 7.149973 ACACTAGTGTCAAAAACGCTCTTATA 58.850 34.615 22.95 0.00 45.69 0.98
4530 4634 5.989777 ACACTAGTGTCAAAAACGCTCTTAT 59.010 36.000 22.95 0.00 45.69 1.73
4531 4635 5.353938 ACACTAGTGTCAAAAACGCTCTTA 58.646 37.500 22.95 0.00 45.69 2.10
4532 4636 4.189231 ACACTAGTGTCAAAAACGCTCTT 58.811 39.130 22.95 0.00 45.69 2.85
4533 4637 3.793559 ACACTAGTGTCAAAAACGCTCT 58.206 40.909 22.95 0.00 45.69 4.09
4534 4638 4.743644 ACTACACTAGTGTCAAAAACGCTC 59.256 41.667 31.11 0.00 45.69 5.03
4547 4651 4.690122 AGCGTTTTTGACACTACACTAGT 58.310 39.130 0.00 0.00 40.28 2.57
4548 4652 4.982916 AGAGCGTTTTTGACACTACACTAG 59.017 41.667 0.00 0.00 0.00 2.57
4549 4653 4.940463 AGAGCGTTTTTGACACTACACTA 58.060 39.130 0.00 0.00 0.00 2.74
4586 4690 9.670442 TCAGGTATTAATGATAACTACTCCCTT 57.330 33.333 0.00 0.00 36.08 3.95
5001 5107 1.533625 AGCCGCTGCATAAGTTTGAA 58.466 45.000 2.05 0.00 41.13 2.69
5051 5157 2.158696 AGAAACACTTGCCTCTTCTGCT 60.159 45.455 0.00 0.00 0.00 4.24
5152 5258 7.952368 AGGCCTTTAAAATATGGATCAGCTAAT 59.048 33.333 0.00 0.00 0.00 1.73
5403 5510 6.659242 AGAACGGATCAGTTATGAAAATTGGT 59.341 34.615 11.37 0.00 39.39 3.67
5469 5576 3.119352 CCTCCAAGTTAGCAAATTGCCTC 60.119 47.826 15.04 5.51 46.52 4.70
5669 5776 5.846164 TCCATAGTACCATGAGATCACCAAT 59.154 40.000 2.55 0.00 0.00 3.16
5702 5809 3.424703 ACCTGACCATCTTTTGTCATGG 58.575 45.455 0.00 0.00 44.68 3.66
5760 5867 6.325596 TGAGTGACAGTCTCTGAAATTATCG 58.674 40.000 9.92 0.00 35.18 2.92
6193 6300 1.647545 CCATGAAACGCTGCATCGGT 61.648 55.000 15.16 4.39 0.00 4.69
6280 6387 3.177228 ACCAGTCCTTTCTGCTACATCT 58.823 45.455 0.00 0.00 34.47 2.90
6413 6520 4.970860 AGTAGCCATTGCACTAGATCAT 57.029 40.909 0.00 0.00 41.13 2.45
6429 6536 2.232208 AGCCAAGCATTTTGGAAGTAGC 59.768 45.455 9.99 0.00 42.06 3.58
6431 6538 4.082245 GCTAAGCCAAGCATTTTGGAAGTA 60.082 41.667 9.99 0.00 42.06 2.24
6460 6567 9.449719 AAGTACTTCGATTCTTCCATGTTATTT 57.550 29.630 1.12 0.00 0.00 1.40
6536 6643 3.099905 ACATCAACTTCCTCCTCGATCA 58.900 45.455 0.00 0.00 0.00 2.92
6604 6711 1.279496 TGGCAGCTAGATCAACAGGT 58.721 50.000 0.00 0.00 0.00 4.00
6646 6753 1.203287 GCTTTTCCCCTTAGCAGCAAG 59.797 52.381 0.00 0.00 35.05 4.01
6723 6830 5.949354 AGTTCACCATTTCCATTATTCCGAA 59.051 36.000 0.00 0.00 0.00 4.30
6957 7065 3.056607 CCCCCAAAACTAGCTGTTCATTG 60.057 47.826 0.00 2.03 38.03 2.82
6965 7073 2.316108 CAACAACCCCCAAAACTAGCT 58.684 47.619 0.00 0.00 0.00 3.32
7025 7133 8.677148 TTGCTCTTTTATGTTTCTACTGTTCT 57.323 30.769 0.00 0.00 0.00 3.01
7045 7153 4.517285 TGGAAATGATCAGTACCTTGCTC 58.483 43.478 0.09 0.00 0.00 4.26
7135 7243 2.992593 TGTAGTGTGGTCTTGCAAACA 58.007 42.857 0.00 0.00 0.00 2.83
7221 7335 8.044908 ACTCATTTTAGTTCGTATGTAACCCAT 58.955 33.333 0.00 0.00 37.58 4.00
7222 7336 7.332430 CACTCATTTTAGTTCGTATGTAACCCA 59.668 37.037 0.00 0.00 0.00 4.51
7224 7338 8.470040 TCACTCATTTTAGTTCGTATGTAACC 57.530 34.615 0.00 0.00 0.00 2.85
7225 7339 9.737025 GTTCACTCATTTTAGTTCGTATGTAAC 57.263 33.333 0.00 0.00 0.00 2.50
7226 7340 9.478768 TGTTCACTCATTTTAGTTCGTATGTAA 57.521 29.630 0.00 0.00 0.00 2.41
7265 7379 8.539117 TCTTTTCTCAGATGGATATAGACACA 57.461 34.615 0.00 0.00 0.00 3.72
7272 7386 8.646900 GGAGTAGTTCTTTTCTCAGATGGATAT 58.353 37.037 0.00 0.00 0.00 1.63
7280 7394 7.411486 TCATAGGGAGTAGTTCTTTTCTCAG 57.589 40.000 0.00 0.00 0.00 3.35
7281 7395 7.979786 ATCATAGGGAGTAGTTCTTTTCTCA 57.020 36.000 0.00 0.00 0.00 3.27
7317 7431 6.681729 TCACAAATACAAGTTCTACTCCCT 57.318 37.500 0.00 0.00 0.00 4.20
7344 7458 7.660208 TGACTAAGTTTTCAAATGTACTCCCTC 59.340 37.037 0.00 0.00 0.00 4.30


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.